KFWins2022's repositories
binCrisp
Find CRISPRS in genomes using pilercr & draws a matrix
bonito
A PyTorch Basecaller for Oxford Nanopore Reads
canu
A single molecule sequence assembler for genomes large and small.
pan-genome-analysis
Processing pipeline for pan-genome visulization and exploration
pbbioconda
PacBio Secondary Analysis Tools on Bioconda
minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences (Not mine, just important for the tutorials)
bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
DegenPrimer
DegenPrimer is a tool to check the quality of degenerate primers by simulating PCR
Roary
Rapid large-scale prokaryote pan genome analysis
pilon
Pilon is an automated genome assembly improvement and variant detection tool
deepsignal
Detecting methylation using signal-level features from Nanopore sequencing reads
prokka
:zap: :aquarius: Rapid prokaryotic genome annotation
ANT
Ambiguous Nucleotide Tool (ANT), software for generating and evaluating degenerate codons for natural and expanded genetic codes.
tombo
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
acPCoA
Adjustment for Confounding Factors using Principal Coordinate Analysis
ProkEvo
ProkEvo - an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses.
SeqSero2
SeqSero2
Salphagome
Novel Discovery of Phages from Salmonella Sequences
plascad
Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.
microbiome_helper
A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
samclip
Filter SAM file for soft and hard clipped alignments
deepSignalingPathwayPrediction
Pathway prediction methylation
ont_tutorial_basicqc
A bioinformatics tutorial demonstrating a best-practice workflow to review a flowcell's sequence_summary.txt
GeneMates
An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences
SeqNet
An R package for simulating RNA-sequence datasets from regulatory networks
DEGEPRIME
A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies
phageParser
A project to extract CRISPR information from open genetic data.